By Stephanie Nebehay and Denis Dumo

GENEVA/JUBA (Reuters) - Tens of thousands of people have fled a fresh outbreak of violence in South Sudan, reporting mass killings, looting and forced recruitment of child soldiers, U.N. agencies said on Tuesday.

Many of the refugees pouring into neighboring Uganda, Kenya and Sudan have been carrying malnourished children, the refugee agency the UNHCR added, the victims of a humanitarian crisis exacerbated by food shortages and a cholera outbreak.

The world's newest nation has been caught up in more than two years of ethnically charged fighting between supporters of President Salva Kiir and his long-time rival Riek Machar that has raised fears of wider instability across east Africa.

Machar's supporters said at least nine people had died in the latest clashes on a road in Central Equatoria state, the region that includes the capital Juba, over the weekend.

Government spokesman Michael Makuei Lueth played down those reports, insisting that a frequently broken peace deal signed last year was still on track. “People must understand that the peace agreement doesn’t belong to Riek Machar," he told reporters in the capital on Tuesday.

The personal rivalry between Kiir, from the Dinka group, and Machar, a Nuer, has worsened ethnic splits in a country awash with weapons since the long civil war that led to its separation from Sudan in 2011.

Machar, who returned to the capital in April under the terms of the troubled peace deal, left again last month as new clashes broke out between his men and Kiir's.

GUNS, OIL, CHOLERA

Government military helicopters flew over the capital over the weekend, but the streets were quiet on Tuesday. Residents reported sharp rises in the prices of fuel, vegetables, flour and other basic foodstuffs, with traders blaming shortages on blockages on the main trade route to Uganda.

Banks closed their branches and many families stayed in shelters outside U.N. compounds across the city.

Further afield, local militias, who often fight over control of land, grazing and oil-producing areas, have been taking advantage of the chaos to step up their operations.

U.N. agencies said refugees had reported gunmen trying to block their flight and harassing them on the way.

"Armed groups operating across different parts of South Sudan are looting villages, murdering civilians and forcibly recruiting young men and boys into their ranks," UNHCR spokeswoman Melissa Fleming told a briefing in Geneva.

Around 60,000 people have fled as violence mounted over the past three weeks, she said, the bulk of them to Uganda, doubling the flow over that border over the past 10 days.

"We are very concerned about quickly having the capacity to treat the increasing numbers of malnourished children who are coming across," Fleming said.

A further 1.6 million South Sudanese are displaced people within their country, said Jens Laerke of the U.N. Office for Humanitarian Affairs (OCHA).

"These are really very vast numbers, it's a massive crisis," Laerke added, noting that in all 900,000 refugees have fled South Sudan since December 2013.

A cholera outbreak is spreading in South Sudan, the World Health Organization (WHO) said, with 35 new admissions being recorded in Juba county daily, WHO spokeswoman Fadela Chaib said.

There have been signs of a split within Machar's movement since he left the capital, and analysts have questioned whether both men have full authority over their followers.

(Editing by Andrew Heavens)